6e16 - Revision history

OCA at 14:38, 13 March 2024

OCA — Wed, 13 Mar 2024 14:38:44 GMT

←Older revision		Revision as of 14:38, 13 March 2024
Line 3:		Line 3:
	<StructureSection load='6e16' size='340' side='right'caption='[[6e16]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='6e16' size='340' side='right'caption='[[6e16]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6e16]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6E16 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6E16 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6e16]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Saccharomyces_cerevisiae_S288C Saccharomyces cerevisiae S288C]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6E16 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6E16 FirstGlance]. <br>
-	</td></tr><tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>SPT15, BTF1, TBP1, YER148W ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id~~=9606 HUMAN])</td></tr>~~	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2.4Å</td></tr>
-	~~<tr id='activity'><td class~~="~~sblockLbl~~">~~<b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>~~[~~http://en.wikipedia.org/wiki/Histone_acetyltransferase Histone acetyltransferase~~]~~, with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=~~2.~~3.1.48 2.3.1.48] </span>~~</td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=6e16 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6e16 OCA], [https://pdbe.org/6e16 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6e16 RCSB], [https://www.ebi.ac.uk/pdbsum/6e16 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6e16 ProSAT]</span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6e16 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6e16 OCA], [~~http~~://pdbe.org/6e16 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6e16 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6e16 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6e16 ProSAT]</span></td></tr>	+
	</table>		</table>
		+	== Disease ==
		+	[https://www.uniprot.org/uniprot/MYC_HUMAN MYC_HUMAN] Note=Overexpression of MYC is implicated in the etiology of a variety of hematopoietic tumors. Note=A chromosomal aberration involving MYC may be a cause of a form of B-cell chronic lymphocytic leukemia. Translocation t(8;12)(q24;q22) with BTG1. Defects in MYC are a cause of Burkitt lymphoma (BL) [MIM:[https://omim.org/entry/113970 113970]. A form of undifferentiated malignant lymphoma commonly manifested as a large osteolytic lesion in the jaw or as an abdominal mass. Note=Chromosomal aberrations involving MYC are usually found in Burkitt lymphoma. Translocations t(8;14), t(8;22) or t(2;8) which juxtapose MYC to one of the heavy or light chain immunoglobulin gene loci.
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/~~TAF1_YEAST TAF1_YEAST~~]~~] Functions as a component~~ of the DNA-binding general transcription factor complex TFIID. Binding of TFIID to a promoter (with or without TATA element) is the initial step in ~~pre-initiation~~ complex (PIC) formation. TFIID plays a key role in the regulation of gene expression by RNA polymerase II through different activities such as transcription activator interaction, core promoter recognition and selectivity, TFIIA and TFIIB interaction, chromatin modification (histone acetylation by TAF1), facilitation of DNA opening and initiation of transcription.<ref>PMID:~~8980232</ref> <ref>PMID:10788514~~</ref> <ref>PMID:12138208</ref> <ref>PMID:12516863</ref>	+	[https://www.uniprot.org/uniprot/TBP_YEAST TBP_YEAST] General transcription factor that functions at the core of the DNA-binding general transcription factor complex TFIID. Binding of TFIID to a promoter (with or without TATA element) is the initial step in preinitiation complex (PIC) formation. TFIID plays a key role in the regulation of gene expression by RNA polymerase II through different activities such as transcription activator interaction, core promoter recognition and selectivity, TFIIA and TFIIB interaction, chromatin modification (histone acetylation by TAF1), facilitation of DNA opening and initiation of transcription.<ref>PMID:9618449</ref> <ref>PMID:12138208</ref> <ref>PMID:12516863</ref> [https://www.uniprot.org/uniprot/TAF1_YEAST TAF1_YEAST] Functions as a component of the DNA-binding general transcription factor complex TFIID. Binding of TFIID to a promoter (with or without TATA element) is the initial step in pre-initiation complex (PIC) formation. TFIID plays a key role in the regulation of gene expression by RNA polymerase II through different activities such as transcription activator interaction, core promoter recognition and selectivity, TFIIA and TFIIB interaction, chromatin modification (histone acetylation by TAF1), facilitation of DNA opening and initiation of transcription.<ref>PMID:8980232</ref> <ref>PMID:10788514</ref> <ref>PMID:12138208</ref> <ref>PMID:12516863</ref> [https://www.uniprot.org/uniprot/MYC_HUMAN MYC_HUMAN] Participates in the regulation of gene transcription. Binds DNA in a non-specific manner, yet also specifically recognizes the core sequence 5'-CAC[GA]TG-3'. Seems to activate the transcription of growth-related genes.
-	~~<div style="background-color~~:~~#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	~~Transcription factor c-MYC is~~ a ~~potent oncoprotein; however,~~ the ~~mechanism of transcriptional regulation via MYC-protein interactions remains poorly understood. The TATA~~-binding ~~protein (TBP) is an essential component of the~~ transcription ~~initiation~~ complex TFIID ~~and is required for gene expression~~. We identify two discrete regions mediating MYC-TBP interactions using structural, biochemical and cellular approaches. A 2.4 -A resolution crystal structure reveals that human MYC amino acids 98-111 interact with TBP in the presence of ~~the amino-terminal domain 1 of TBP-associated factor 1~~ (~~TAF1(TAND1~~)~~). Using biochemical approaches, we have shown that MYC amino acids 115~~-~~124 also interact with TBP independently of TAF1~~(~~TAND1~~). ~~Modeling reveals that this region of MYC resembles~~ a ~~TBP anchor motif found~~ in factors that regulate TBP promoter loading. Site-specific MYC mutants that abrogate MYC-TBP interaction compromise MYC activity. We propose that MYC-TBP interactions propagate transcription by modulating the ~~energetic landscape~~ of transcription ~~initiation complex assembly.~~	+
-		+
-	~~Multiple direct interactions of TBP with the MYC oncoprotein.~~,~~Wei Y~~, ~~Resetca D~~, ~~Li Z, Johansson-Akhe I, Ahlner A, Helander S, Wallenhammar A, Morad V, Raught B, Wallner B, Kokubo T, Tong Y, Penn LZ, Sunnerhagen M Nat Struct Mol Biol. 2019 Nov;26~~(11)~~:1035-1043. doi: 10.1038/s41594-019-0321-z.~~, ~~Epub 2019 Nov 4~~. PMID:~~31686052~~<ref>PMID:~~31686052~~</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.~~<br>	+
-	</~~div~~>	+
-	<~~div class="pdbe-citations 6e16" style="background-color:#fffaf0;"~~></~~div~~>	+
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Histone acetyltransferase]]~~	+	[[Category: Homo sapiens]]
-	~~[[Category: Human~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Arrowsmith, C H~~]]	+	[[Category: Saccharomyces cerevisiae S288C]]
-	[[Category: ~~Dong, A~~]]	+	[[Category: Arrowsmith CH]]
-	[[Category: ~~Edwards,~~ A M]]	+	[[Category: Dong A]]
-	[[Category: ~~Penn, L~~]]	+	[[Category: Edwards AM]]
-	[[Category: ~~Structural genomic~~]]	+	[[Category: Penn L]]
-	[[Category: Sunnerhagen, M]]	+	[[Category: Sunnerhagen M]]
-	[[Category: Tong, Y]]	+	[[Category: Tong Y]]
-	[[Category: Wei, Y]]	+	[[Category: Wei Y]]
-	~~[[Category: Carcinogenesis]]~~	+
-	~~[[Category: Dna binding protein]]~~	+
-	~~[[Category: Transcriptional regulation~~]]	+

OCA at 17:23, 20 November 2019

OCA — Wed, 20 Nov 2019 17:23:10 GMT

←Older revision		Revision as of 17:23, 20 November 2019
Line 3:		Line 3:
	<StructureSection load='6e16' size='340' side='right'caption='[[6e16]], [[Resolution\|resolution]] 2.40Å' scene=''>		<StructureSection load='6e16' size='340' side='right'caption='[[6e16]], [[Resolution\|resolution]] 2.40Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6e16]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6E16 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6E16 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6e16]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6E16 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6E16 FirstGlance]. <br>
-	</td></tr><tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Histone_acetyltransferase Histone acetyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.1.48 2.3.1.48] </span></td></tr>	+	</td></tr><tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">SPT15, BTF1, TBP1, YER148W ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Histone_acetyltransferase Histone acetyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.1.48 2.3.1.48] </span></td></tr>
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6e16 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6e16 OCA], [http://pdbe.org/6e16 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6e16 RCSB], [http://www.ebi.ac.uk/pdbsum/6e16 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6e16 ProSAT]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6e16 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6e16 OCA], [http://pdbe.org/6e16 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6e16 RCSB], [http://www.ebi.ac.uk/pdbsum/6e16 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6e16 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/TAF1_YEAST TAF1_YEAST]] Functions as a component of the DNA-binding general transcription factor complex TFIID. Binding of TFIID to a promoter (with or without TATA element) is the initial step in pre-initiation complex (PIC) formation. TFIID plays a key role in the regulation of gene expression by RNA polymerase II through different activities such as transcription activator interaction, core promoter recognition and selectivity, TFIIA and TFIIB interaction, chromatin modification (histone acetylation by TAF1), facilitation of DNA opening and initiation of transcription.<ref>PMID:8980232</ref> <ref>PMID:10788514</ref> <ref>PMID:12138208</ref> <ref>PMID:12516863</ref>		[[http://www.uniprot.org/uniprot/TAF1_YEAST TAF1_YEAST]] Functions as a component of the DNA-binding general transcription factor complex TFIID. Binding of TFIID to a promoter (with or without TATA element) is the initial step in pre-initiation complex (PIC) formation. TFIID plays a key role in the regulation of gene expression by RNA polymerase II through different activities such as transcription activator interaction, core promoter recognition and selectivity, TFIIA and TFIIB interaction, chromatin modification (histone acetylation by TAF1), facilitation of DNA opening and initiation of transcription.<ref>PMID:8980232</ref> <ref>PMID:10788514</ref> <ref>PMID:12138208</ref> <ref>PMID:12516863</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Transcription factor c-MYC is a potent oncoprotein; however, the mechanism of transcriptional regulation via MYC-protein interactions remains poorly understood. The TATA-binding protein (TBP) is an essential component of the transcription initiation complex TFIID and is required for gene expression. We identify two discrete regions mediating MYC-TBP interactions using structural, biochemical and cellular approaches. A 2.4 -A resolution crystal structure reveals that human MYC amino acids 98-111 interact with TBP in the presence of the amino-terminal domain 1 of TBP-associated factor 1 (TAF1(TAND1)). Using biochemical approaches, we have shown that MYC amino acids 115-124 also interact with TBP independently of TAF1(TAND1). Modeling reveals that this region of MYC resembles a TBP anchor motif found in factors that regulate TBP promoter loading. Site-specific MYC mutants that abrogate MYC-TBP interaction compromise MYC activity. We propose that MYC-TBP interactions propagate transcription by modulating the energetic landscape of transcription initiation complex assembly.
		+
		+	Multiple direct interactions of TBP with the MYC oncoprotein.,Wei Y, Resetca D, Li Z, Johansson-Akhe I, Ahlner A, Helander S, Wallenhammar A, Morad V, Raught B, Wallner B, Kokubo T, Tong Y, Penn LZ, Sunnerhagen M Nat Struct Mol Biol. 2019 Nov;26(11):1035-1043. doi: 10.1038/s41594-019-0321-z., Epub 2019 Nov 4. PMID:31686052<ref>PMID:31686052</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6e16" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
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	</StructureSection>		</StructureSection>
	[[Category: Histone acetyltransferase]]		[[Category: Histone acetyltransferase]]
		+	[[Category: Human]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Arrowsmith, C H]]		[[Category: Arrowsmith, C H]]

OCA at 10:17, 2 October 2019

OCA — Wed, 02 Oct 2019 10:17:41 GMT

←Older revision		Revision as of 10:17, 2 October 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6e16 is ~~ON HOLD until Paper Publication~~	+	==Ternary structure of c-Myc-TBP-TAF1==
-		+	<StructureSection load='6e16' size='340' side='right'caption='[[6e16]], [[Resolution\|resolution]] 2.40Å' scene=''>
-	~~Authors~~:	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6e16]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6E16 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6E16 FirstGlance]. <br>
-	~~Description~~:	+	</td></tr><tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Histone_acetyltransferase Histone acetyltransferase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.3.1.48 2.3.1.48] </span></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6e16 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6e16 OCA], [http://pdbe.org/6e16 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6e16 RCSB], [http://www.ebi.ac.uk/pdbsum/6e16 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6e16 ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/TAF1_YEAST TAF1_YEAST]] Functions as a component of the DNA-binding general transcription factor complex TFIID. Binding of TFIID to a promoter (with or without TATA element) is the initial step in pre-initiation complex (PIC) formation. TFIID plays a key role in the regulation of gene expression by RNA polymerase II through different activities such as transcription activator interaction, core promoter recognition and selectivity, TFIIA and TFIIB interaction, chromatin modification (histone acetylation by TAF1), facilitation of DNA opening and initiation of transcription.<ref>PMID:8980232</ref> <ref>PMID:10788514</ref> <ref>PMID:12138208</ref> <ref>PMID:12516863</ref>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Histone acetyltransferase]]
		+	[[Category: Large Structures]]
		+	[[Category: Arrowsmith, C H]]
		+	[[Category: Dong, A]]
		+	[[Category: Edwards, A M]]
		+	[[Category: Penn, L]]
		+	[[Category: Structural genomic]]
		+	[[Category: Sunnerhagen, M]]
		+	[[Category: Tong, Y]]
		+	[[Category: Wei, Y]]
		+	[[Category: Carcinogenesis]]
		+	[[Category: Dna binding protein]]
		+	[[Category: Transcriptional regulation]]

OCA at 10:19, 16 January 2019

OCA — Wed, 16 Jan 2019 10:19:02 GMT

←Older revision		Revision as of 10:19, 16 January 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6e16 is ON HOLD	+	The entry 6e16 is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "6e16" [edit=sysop:move=sysop]

OCA — Wed, 18 Jul 2018 05:38:36 GMT

Protected "6e16" [edit=sysop:move=sysop]

←Older revision

Revision as of 05:38, 18 July 2018

OCA: New page: '''Unreleased structure''' The entry 6e16 is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 18 Jul 2018 05:38:35 GMT

New page: '''Unreleased structure''' The entry 6e16 is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6e16 is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]